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How to install Python 3 and required modules on Linux

Install Python 3

First check and update any existing Python installations:

sudo apt-get install
sudo apt-get update
sudo apt-get -y upgrade

Check which version of Python3 you have:

python3 -v

If you do not have python3, please install using:

sudo apt-get install python3

#Install pip

pip is a package manager for python. To install:

sudo apt-get install -y python3-pip

Install modules

Open Terminal and type:

pip3 install [modulename]

for example:

pip3 install biopython

will install Biopython.

Please repeat and use pip3 to install all the required modules for ciderseq (see Readme)

Install MUSCLE

  • Download Muscle from:www.drive5.com/muscle/downloads.htm
  • Extract the file and copy to your cider-seq folder.
  • Rename the file to 'muscle'
  • If placed in another folder, make sure you edit the path address in the ciderseq_config.json file.

Install BLAST

  • Download the latest blast file from: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
  • Extract the tar.gz file to any location on your machine:
tar -xzvf [blast filename].tar.gz -C [/target/directory]
  • Export the BLAST executables to your path by using the following commands:
export PATH=$PATH:[/target/directory]